Boeing could end up with serious problems, aviation expert Michael Boyd told CNBC on Thursday, if it turns out the battery concern that prompted the U.S. Federal Aviation Administration to ground the new 787 Dreamliners is a "design flaw."

Jason Gursky, aerospace and defense analyst at Citigroup, agreed with Boyd in a "Squawk Box" interview. "If this is a manufacturing issue, we probably get a quick fix," he said. "If it's a design issue, probably takes a little more time and it would be a little more damaging to the overall outlook for the aircraft in the near term."

Boyd, chairman of The Boyd Group, made a comparison to past new plane rollouts. "Is it going to be like [Boeing's] 747 40 years ago, where they had major problems and they worked it out," Boyd asked, "or is it going to be on the other end like a Lockheed Electra that basically put the company out of the passenger airplane business?"

Yuzuru Yoshikawa | Bloomberg | Getty Images

787 Dreamliner aircraft operated by All Nippon Airways Co. (ANA) stands on the tarmac after making an emergency landing in Takamatsu, Japan.

He said he doesn't believe the Dreamliner is going to be the Electra. "[But] if this airplane really has a problem, it's going to cost Boeing a lot of money. And it may be a loss leader for them going forward for the next several years, if they're not careful," he said, adding that "Boeing is in some deep flavored yogurt."

Regulators around the world followed the Wednesday night FAA order, which it delivered after battery issues caused the emergency landing of an All Nippon Airways Dreamliner earlier in the day in Japan and a fire on a Japan Airlines 787 parked in Boston on January 7.

"Unfortunately for Boeing shares, we're probably gated here today for the next three months until this review is done," said Citi's Gursky, who advised owners of Boeing stock to hold shares at this point because airlines and customers have a lot invested in the Dreamliner. "Over the next month. I think we're going to get a nice entry point on the stock."

So far, there are only six 787s released in the U.S. — all operated by United Continental — out of about 6,200 planes. The problems for United and American Airlines could come down the line because they have put in a lot of Dreamliner orders, Boyd said.

"But if you're Japan Airlines or worse All Nippon, you've got a big chunk of your fleet down and that's a lot of revenue going out the door." Boyd also estimated that it could be costing ANA $20-30 million a day in net revenue.